After attending art school and working as a parking valet and other odd jobs for nightclubs,[9] Mooney went to New York City in 1940 to enter the fledgling comic-book field. Following his first assignment, the new feature "The Moth" in Fox Publications' Mystery Men Comics #9-12 (April–July 1940), Mooney worked for the comic-book packager Eisner & Iger, one of the studios that would supply outsourced comics to publishers testing the waters of the new medium. He left voluntarily after two weeks: "I was just absolutely crestfallen when I looked at some of the guys’ work. Lou Fine was working there, Nick Cardy ... and Eisner himself. I was beginning to feel that I was way, way in beyond my depth...." [9]

Mooney went on staff at Fiction House for approximately nine months, working on features including "Camilla" and "Suicide Smith" and becoming friends with colleagues George Tuska, Ruben Moreira, and Cardy. He began freelancing for Timely Comics, the 1940s predecessor of Marvel, working on that company's "animation" line of funny animal and movie-cartoon tie-in comics.

As Mooney describes his being hired by editor-in-chief and art director Stan Lee:

I met Stan the first time when I was looking for work at Timely. . . . I came in, being somewhat young and cocky at the time, and Stan asked me what I did. I said I penciled; he said, 'What else?' I said I inked. He said, 'What else?' I said, 'Color.' 'Do anything else?' I said, 'Yeah, I letter, too.' He said, 'Do you print the damn books, too?' I guess he was about two or three years my junior at that point. I think I was about 21 or 22.[10]

In 1946, Mooney began a 22-year association with the company that would evolve into DC. He began with the series Batman[12] as a ghost artist for credited artist Bob Kane. As Mooney recalled of coming to DC,

[T]he funny animal stuff was no longer in demand, and an awful lot of us were scurrying around looking for work . . . and I heard on the grapevine that they were looking for an artist to do Batman. So I buzzed up there to DC, talked to them and showed them my stuff, and even though they weren't so sure because of my funny-animal background, they gave me a shot at it. I brought the work in, and [editor] Whitney Ellsworth said, 'OK, you're on'. . . . [I]t was ghosting. [Prominent Batman ghost-artist] Dick Sprang [had] taken off and wanted to do something else. So Dick took off for Arizona, and DC was looking for someone to fill in. So, that's where I fit in, and I stayed on Batman for quite a few years. . . .[10]

Most notably, Mooney drew the backup feature "Supergirl" in Action Comics from 1959 to 1968.[15] For much of this run on his signature character, Mooney lived in Los Angeles, managing an antiquarianbook store on Hollywood Boulevard and sometimes hiring art students to work in the store and ink backgrounds on his pencilled pages.[4] By 1968, he had moved back to New York, where DC, he recalled, was

... getting into the illustrative type of art then, primarily Neal Adams, and they wanted to go in that direction. Towards the end there I picked up on it and I think my later 'Supergirl' was quite illustrative, but not quite what they wanted. I knew the handwriting was on the wall, so I was looking around.... The reason I hadn't worked at Marvel for all those years was because they didn't pay as well as DC. ... I think at that time [it] was $30 [a page] when I was getting closer to $50 at DC".[9]

As a penciler, Mooney did several issues of Peter Parker, the Spectacular Spider-Man, as well as Spider-Man stories in Marvel Team-Up, and he both penciled and inked issues of writer Steve Gerber's Man-Thing and the entire 10-issue run of Gerber's cult-hit Omega the Unknown,[19][20] among many other titles. Mooney named his collaborations with Gerber as being among his personal favorites.[21] In 2010, Comics Bulletin ranked Gerber and Mooney's run on Omega the Unknown tenth on its list of the "Top 10 1970s Marvels".[22]Carrion debuted in The Spectacular Spider-Man #25 (Dec. 1978) by Bill Mantlo and Mooney.[23] Writer Ralph Macchio and Mooney introduced the Rapier in The Spectacular Spider-Man Annual #2 (1980).[24]

In 1975, Mooney, wanting to move to Florida, negotiated a 10-year contract with Marvel to supply artwork from there. "It was a good deal. The money wasn't too great, but I was paid every couple of weeks, I had insurance, and I had a lot of security that most freelancers never had".[10] That same year, Mooney and his wife, Anne, had a daughter, Nolle.[25]

^Manning "1960s" in Gilbert (2012), p. 45: "Written by Lee with art by Romita and Mooney...Randy Robertson made his debut. The son of city editor Randy Robertson, he would go on to be the first African American member of Peter Parker's group of friends."

^Manning "1960s" in Gilbert (2012), p. 49: "In this tale written by [Stan] Lee and drawn by the team of John Buscema and Jim Mooney, window washer Hobie Brown became fed up with his dead-end job and used his inventive mind to craft the identity and weapons of the Prowler."

^Sanderson, Peter; Gilbert, Laura, ed. (2008). "1970s". Marvel Chronicle A Year by Year History. London, United Kingdom: Dorling Kindersley. p. 175. ISBN978-0756641238. In March [1976], a new super hero series began called Omega the Unknown, created by writers Steve Gerber and Mary Skrenes and artist Jim Mooney. The title character was an alien humanoid, who rarely spoke and served as protector to an eerily precocious young boy.CS1 maint: extra text: authors list (link)

^Stroud, Bryan D. (2007). "The Silver Age Sage". WTV-Zone.com. Archived from the original on August 29, 2012. Retrieved November 25, 2013. I loved working with Steve Gerber and Omega to a certain extent, too, but Man-Thing was one of my very favorites.Cite uses deprecated parameter |deadurl= (help)

^Manning "1970s" in Gilbert (2012), p. 105: "The ghost of Miles Warren, the villainous Jackal, came to call - in a fashion - in this story written by Bill Mantlo and drawn by Jim Mooney."

^Manning "1980s" in Gilbert (2012), p. 115: "Although this issue by writer Ralph Macchio and artist Jim Mooney would prove a strong case for the character, he would be destined for a short career in the comic book world."